Program title: ProtoMD
Catalogue identifier: AEZN_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEZN_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: GNU General Public License, version 3
No. of lines in distributed program, including test data, etc.: 281345
No. of bytes in distributed program, including test data, etc.: 3706191
Distribution format: tar.gz
Programming language: Python 2.7.3.
Computer: x86/x86 64.
Operating system: Linux.
RAM: Depends on the size of the system being simulated and duration of the simulation (few MBs to TBs)
Classification: 3, 4.12, 16.9, 23.
External routines: GROMACS (tested with versions 4.6x and 5.0x), MDAnalysis, GromacsWrapper, numpy, scipy, MPI
Nature of problem: Prototyping multiscale coarse-grained algorithms for molecular dynamics.
Solution method: Combining the open-source GROMACS molecular dynamics package and the python-based MDAnalysis library for running, debugging, and analyzing multiscale simulations
Restrictions: The system under study must be characterized by a clear separation of timescales; otherwise, the multiscale algorithm fails to capture the slowly-varying modes.
Running time: Depending on the problem size, simulations can take few hours to months.